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Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
Tamura K, Nei M. Tamura K, et al. Among authors: nei m. Mol Biol Evol. 1993 May;10(3):512-26. doi: 10.1093/oxfordjournals.molbev.a040023. Mol Biol Evol. 1993. PMID: 8336541
The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data.
Katsura Y, Stanley CE Jr, Kumar S, Nei M. Katsura Y, et al. Among authors: nei m. Mol Biol Evol. 2017 Mar 1;34(3):718-723. doi: 10.1093/molbev/msw272. Mol Biol Evol. 2017. PMID: 28100791 Free PMC article.
Efficiencies of the NJp, Maximum Likelihood, and Bayesian Methods of Phylogenetic Construction for Compositional and Noncompositional Genes.
Yoshida R, Nei M. Yoshida R, et al. Among authors: nei m. Mol Biol Evol. 2016 Jun;33(6):1618-24. doi: 10.1093/molbev/msw042. Epub 2016 Feb 28. Mol Biol Evol. 2016. PMID: 26929244
This c is given by Pc (1 - dT/dTmax) = Pc (m - 3 - dT/2)/(m - 3), where m is the number of taxa used and dTmax is the maximum possible value of dT, which is given by 2(m - 3). ...
This c is given by Pc (1 - dT/dTmax) = Pc (m - 3 - dT/2)/(m - 3), where m is the number of taxa used and dTmax is the m …
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. Tamura K, et al. Among authors: nei m. Mol Biol Evol. 2011 Oct;28(10):2731-9. doi: 10.1093/molbev/msr121. Epub 2011 May 4. Mol Biol Evol. 2011. PMID: 21546353 Free PMC article.
POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface.
Takezaki N, Nei M, Tamura K. Takezaki N, et al. Among authors: nei m. Mol Biol Evol. 2010 Apr;27(4):747-52. doi: 10.1093/molbev/msp312. Epub 2009 Dec 18. Mol Biol Evol. 2010. PMID: 20022889 Free PMC article.
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
Tamura K, Dudley J, Nei M, Kumar S. Tamura K, et al. Among authors: nei m. Mol Biol Evol. 2007 Aug;24(8):1596-9. doi: 10.1093/molbev/msm092. Epub 2007 May 7. Mol Biol Evol. 2007. PMID: 17488738
False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus.
Suzuki Y, Nei M. Suzuki Y, et al. Among authors: nei m. Mol Biol Evol. 2004 May;21(5):914-21. doi: 10.1093/molbev/msh098. Epub 2004 Mar 10. Mol Biol Evol. 2004. PMID: 15014169
Evolutionary change of the numbers of homeobox genes in bilateral animals.
Nam J, Nei M. Nam J, et al. Among authors: nei m. Mol Biol Evol. 2005 Dec;22(12):2386-94. doi: 10.1093/molbev/msi229. Epub 2005 Aug 3. Mol Biol Evol. 2005. PMID: 16079247 Free PMC article.
Reliabilities of identifying positive selection by the branch-site and the site-prediction methods.
Nozawa M, Suzuki Y, Nei M. Nozawa M, et al. Among authors: nei m. Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6700-5. doi: 10.1073/pnas.0901855106. Epub 2009 Apr 1. Proc Natl Acad Sci U S A. 2009. PMID: 19339501 Free PMC article.
Prospects for inferring very large phylogenies by using the neighbor-joining method.
Tamura K, Nei M, Kumar S. Tamura K, et al. Among authors: nei m. Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):11030-5. doi: 10.1073/pnas.0404206101. Epub 2004 Jul 16. Proc Natl Acad Sci U S A. 2004. PMID: 15258291 Free PMC article.
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